from rdkit import Chem
from ..utils.base_tool import BaseTool
from ..utils.errors import ChemMCPInputError
from ..utils.mcp_app import ChemMCPManager, run_mcp_server
# Constants
# List obtained from https://github.com/rdkit/rdkit/blob/master/Data/FunctionalGroups.txt
DICT_FGS = {
"furan": "o1cccc1",
"aldehydes": " [CX3H1](=O)[#6]",
"esters": " [#6][CX3](=O)[OX2H0][#6]",
"ketones": " [#6][CX3](=O)[#6]",
"amides": " C(=O)-N",
"thiol groups": " [SH]",
"alcohol groups": " [OH]",
"methylamide": "*-[N;D2]-[C;D3](=O)-[C;D1;H3]",
"carboxylic acids": "*-C(=O)[O;D1]",
"carbonyl methylester": "*-C(=O)[O;D2]-[C;D1;H3]",
"terminal aldehyde": "*-C(=O)-[C;D1]",
"amide": "*-C(=O)-[N;D1]",
"carbonyl methyl": "*-C(=O)-[C;D1;H3]",
"isocyanate": "*-[N;D2]=[C;D2]=[O;D1]",
"isothiocyanate": "*-[N;D2]=[C;D2]=[S;D1]",
"nitro": "*-[N;D3](=[O;D1])[O;D1]",
"nitroso": "*-[N;R0]=[O;D1]",
"oximes": "*=[N;R0]-[O;D1]",
"Imines": "*-[N;R0]=[C;D1;H2]",
"terminal azo": "*-[N;D2]=[N;D2]-[C;D1;H3]",
"hydrazines": "*-[N;D2]=[N;D1]",
"diazo": "*-[N;D2]#[N;D1]",
"cyano": "*-[C;D2]#[N;D1]",
"primary sulfonamide": "*-[S;D4](=[O;D1])(=[O;D1])-[N;D1]",
"methyl sulfonamide": "*-[N;D2]-[S;D4](=[O;D1])(=[O;D1])-[C;D1;H3]",
"sulfonic acid": "*-[S;D4](=O)(=O)-[O;D1]",
"methyl ester sulfonyl": "*-[S;D4](=O)(=O)-[O;D2]-[C;D1;H3]",
"methyl sulfonyl": "*-[S;D4](=O)(=O)-[C;D1;H3]",
"sulfonyl chloride": "*-[S;D4](=O)(=O)-[Cl]",
"methyl sulfinyl": "*-[S;D3](=O)-[C;D1]",
"methyl thio": "*-[S;D2]-[C;D1;H3]",
"thiols": "*-[S;D1]",
"thio carbonyls": "*=[S;D1]",
"halogens": "*-[#9,#17,#35,#53]",
"t-butyl": "*-[C;D4]([C;D1])([C;D1])-[C;D1]",
"tri fluoromethyl": "*-[C;D4](F)(F)F",
"acetylenes": "*-[C;D2]#[C;D1;H]",
"cyclopropyl": "*-[C;D3]1-[C;D2]-[C;D2]1",
"ethoxy": "*-[O;D2]-[C;D2]-[C;D1;H3]",
"methoxy": "*-[O;D2]-[C;D1;H3]",
"side-chain hydroxyls": "*-[O;D1]",
"ketones": "*=[O;D1]",
"primary amines": "*-[N;D1]",
"nitriles": "*#[N;D1]",
}
@ChemMCPManager.register_tool
class FunctionalGroups(BaseTool):
__version__ = "0.1.0"
name = "FunctionalGroups"
func_name = 'identify_functional_groups'
description = "Identify functional groups in a molecule."
implementation_description = "Uses RDKit's SMARTS patterns to identify functional groups in a molecule. The tool checks for a comprehensive list of common functional groups including alcohols, aldehydes, ketones, carboxylic acids, and many others."
oss_dependencies = [
("ChemCrow", "https://github.com/ur-whitelab/chemcrow-public", "MIT")
]
services_and_software = []
categories = ["Molecule"]
tags = ["Molecular Information", "RDKit", "SMILES"]
required_envs = []
code_input_sig = [('smiles', 'str', 'N/A', 'SMILES string of the molecule.')]
text_input_sig = [('smiles', 'str', 'N/A', 'SMILES string of the molecule.')]
output_sig = [('fgs', 'str', 'A description of functional groups in the molecule.')]
examples = [
{'code_input': {'smiles': 'CCO'}, 'text_input': {'smiles': 'CCO'}, 'output': {'fgs': 'This molecule contains alcohol groups, and side-chain hydroxyls.'}},
]
def _run_base(self, smiles: str) -> str:
def _is_fg_in_mol(mol, fg):
fgmol = Chem.MolFromSmarts(fg)
mol = Chem.MolFromSmiles(mol.strip())
return len(Chem.Mol.GetSubstructMatches(mol, fgmol, uniquify=True)) > 0
try:
fgs_in_molec = [
name
for name, fg in DICT_FGS.items()
if _is_fg_in_mol(smiles, fg)
]
if len(fgs_in_molec) > 1:
return f"This molecule contains {', '.join(fgs_in_molec[:-1])}, and {fgs_in_molec[-1]}."
elif len(fgs_in_molec) == 1:
return f"This molecule contains {fgs_in_molec[0]}."
else:
return "This molecule does not contain any functional groups."
except:
raise ChemMCPInputError("Invalid SMILES string.")
if __name__ == "__main__":
run_mcp_server()
